#!/usr/bin/runAmos -C
# `minimus' - The AMOS Lightweight Assembler Pipeline

#--------------------------------------- USER DEFINED VALUES ------------------#
TGT = $(strip .frg PREFIX).afg
#------------------------------------------------------------------------------#
PREF = $(strip .frg PREFIX)

BINDIR=/usr/bin

BANK    = $(PREF).bnk
CONTIG  = $(PREF).contig
FASTA   = $(PREF).fasta

## Converting to AFG
10: $(BINDIR)/toAmos -f $(PREFIX) -o $(TGT)

## Building AMOS bank
20: $(BINDIR)/bank-transact -c -z -b $(BANK) -m $(TGT)

## Assembling fragments
30: (export AMOSBIN=$(BINDIR); $(BINDIR)/preassembleFrgs $(BANK))

## Outputting contigs
40: $(BINDIR)/bank2contig $(BANK) > $(CONTIG)

## Converting to FastA file
50: $(BINDIR)/bank2fasta -b $(BANK) > $(FASTA)
